We have used a subtractive procedure to isolate cDNA clones encoding g
enes expressed differentially in ascidian species with alternate modes
of development. The ascidians used in this study were Molgula oculata
, which develops a tailed (urodele) larva, and Molgula occulta, which
develops a tailless (anural) larva. Two of the identified clones, Uro-
2 and Uro-11, are described. Southern blots show that the Uro-2 and Ur
o-11 genes are present in both species, but the corresponding mRNAs ar
e expressed preferentially in the urodele species. In situ hybridizati
on showed that Uro-2 and Uro-11 transcripts accumulate in small oocyte
s during oogenesis. The maternal Uro-2 and Uro-11 transcripts were dis
tributed throughout the oocyte cytoplasm. Transcript concentrations de
clined during vitellogenesis, but mature eggs still contain detectable
levels of Uro-2 and Uro-11 mRNA. After fertilization, the maternal Ur
o-2 and Uro-11 transcripts were localized in the ectoplasm of uncleave
d zygotes and mostly entered the ectoderm cells during cleavage. The U
ro-2 gene appears to produce only maternal transcripts. In contrast, t
he Uro-11 gene may also produce zygotic transcripts, which accumulate
between gastrulation and neurulation in posterior epidermis, neural an
d tail muscle cells. Zygotic expression of the Uro-11 gene was not det
ected in embryos of the anural species. The deduced amino acid sequenc
es of the Uro-2 and Uro-11 cDNAs suggest that they encode novel basic
proteins with distinctive structural features. The predicted Uro-2 pro
tein contains a leucine zipper motif, suggesting that it may dimerize
with another protein. The predicted Uro-11 protein contains a nuclear
localization signal, a region with similarity to part of the DNA-bindi
ng motif in the bacterial histone-like HU and IHF proteins, 12 repeats
of the proposed DNA-binding motif S(T)PXX, and a potential zinc finge
r of the C6 or C6H2 class, suggesting that it may be a DNA-binding pro
tein. The Uro-2 and Uro-11 proteins are candidates for regulatory fact
ors involved in the evolutionary transition from urodele to anural dev
elopment.